gProfileR (version 0.5.3)

gprofiler: Annotate gene list functionally.

Description

Annotate gene list functionally.

Usage

gprofiler(query, organism="hsapiens", ordered_query=F, significant=T,
    exclude_iea=F, region_query=F, max_p_value=1, max_set_size=0,
    correction_method="analytical", hier_filtering="none",
    domain_size="annotated", custom_bg="", numeric_ns="", no_isects=F,
    png_fn, include_graph=F, src_filter)

Arguments

organism

organism name.

query

vector of gene IDs or a list of such vectors.

ordered_query

in case output gene lists are ranked this option may be used to get GSEA style p-values.

significant

whether all or only statistically significant results should be returned.

exclude_iea

exclude electronic annotations (IEA).

region_query

interpret query as chromosomal ranges.

max_p_value

custom p-value threshold, results with a larger p-value are excluded.

max_set_size

maximum size of functional category, larger categories are excluded.

correction_method

the algorithm used for determining the significance threshold, one of "gSCS", "fdr", "bonferroni".

hier_filtering

hierarchical filtering strength, one of "none", "moderate", "strong".

domain_size

statistical domain size, one of "annotated", "known".

custom_bg

vector of gene names to use as a statistical background.

numeric_ns

namespace to use for fully numeric IDs.

no_isects

do not return intersections between query and term, significantly faster for large queries.

png_fn

request the result as PNG image and write it to png_fn.

include_graph

request inclusion of network data with the result.

src_filter

a vector of data sources to use. Currently, these include GO (GO:BP, GO:MF, GO:CC to select a particular GO branch), KEGG, REAC, TF, MI, CORUM, HP. Please see the g:GOSt web tool for the comprehensive list and details on incorporated data sources.

Value

• A data frame with the enrichment analysis results. If the input consisted of several lists the corresponding list is indicated with a variable 'query number'. When requesting a PNG image, either TRUE or FALSE, depending on whether a non-empty result was received and a file written or not, respectively. If 'include_graph' is set, the return value may include the attribute 'networks', containing a list of all network sources, each in turn containing a list of graph edges. The edge structure is a list containing the two interacting symbols and two boolean values (in that order), indicating whether the first or second interactor is part of the input query (core nodes).

Details

Interface to the g:Profiler tool for finding enrichments in gene lists. Organism names are constructed by concatenating the first letter of the name and the family name. Example: human - 'hsapiens', mouse - 'mmusculus'. If requesting PNG output, the request is directed to the g:GOSt tool in case 'query' is a vector and the g:Cocoa (compact view of multiple queries) tool in case 'query' is a list. PNG output can fail (return FALSE) in case the input query is too large. In such case, it is advisable to fall back to a non-image request.

References

J. Reimand, M. Kull, H. Peterson, J. Hansen, J. Vilo: g:Profiler - a web-based toolset for functional profiling of gene lists from large-scale experiments (2007) NAR 35 W193-W200

Examples

gprofiler(c("Klf4", "Pax5", "Sox2", "Nanog"), organism = "mmusculus")